Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 219.01 kDa 
• Atom Count: 14125 
• Modelled Residue Count: 1818 
• Deposited Residue Count: 1934 
• Unique protein chains: 3

3HKB

Tubulin: RB3 Stathmin-like domain complex

• PDB DOI: 10.2210/pdb3HKB/pdb

• Classification: CELL CYCLE
• Organism(s): Ovis aries, Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-23 Released: 2009-09-01 
• Deposition Author(s): Dorleans, A., Gigant, B., Ravelli, R.B.G., Mailliet, P., Mikol, V., Knossow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Variations in the colchicine-binding domain provide insight into the structural switch of tubulin

Dorleans, A., Gigant, B., Ravelli, R.B.G., Mailliet, P., Mikol, V., Knossow, M.

(2009) Proc Natl Acad Sci U S A 106: 13775-13779

• PubMed: 19666559 
• DOI: 10.1073/pnas.0904223106
• Primary Citation of Related Structures:  
  3HKB, 3HKC, 3HKD, 3HKE


• PubMed Abstract: 
  

Structural changes occur in the alphabeta-tubulin heterodimer during the microtubule assembly/disassembly cycle. Their most prominent feature is a transition from a straight, microtubular structure to a curved structure. There is a broad range of small molecule compounds that disturbs the microtubule cycle, a class of which targets the colchicine-binding site and prevents microtubule assembly. This class includes compounds with very different chemical structures, and it is presently unknown whether they prevent tubulin polymerization by the same mechanism. To address this issue, we have determined the structures of tubulin complexed with a set of such ligands and show that they interfere with several of the movements of tubulin subunits structural elements upon its transition from curved to straight. We also determined the structure of tubulin unliganded at the colchicine site; this reveals that a beta-tubulin loop (termed T7) flips into this site. As with colchicine site ligands, this prevents a helix which is at the interface with alpha-tubulin from stacking onto a beta-tubulin beta sheet as in straight protofilaments. Whereas in the presence of these ligands the interference with microtubule assembly gets frozen, by flipping in and out the beta-subunit T7 loop participates in a reversible way in the resistance to straightening that opposes microtubule assembly. Our results suggest that it thereby contributes to microtubule dynamic instability.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Bâtiment 34, 1, avenue de la Terrasse, 91198 Gif sur Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, C	451	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWZ0 (Ovis aries) Explore D0VWZ0  Go to UniProtKB:  D0VWZ0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWY9 (Ovis aries) Explore D0VWY9  Go to UniProtKB:  D0VWY9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	142	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	F [auth A], I [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	H [auth B], K [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	G [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 328.826	α = 90
b = 328.826	β = 90
c = 53.711	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-23 
• Released Date: 2009-09-01 
Deposition Author(s): Dorleans, A., Gigant, B., Ravelli, R.B.G., Mailliet, P., Mikol, V., Knossow, M.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance